THURSDAY, Feb 7 , 12 p.m. 11 JILA AUDITORIUM
Nynke Dekker
Kavli Institute of NanoScience Delft University of Technology
From Single Molecules to the Cell
The double-stranded nature of the DNA helix has important implications for the build-up of torque in biological processes that unravel the helix to read the genetic code. Indeed, excess torque can lead to the formation of coils in the DNA (generally referred to as supercoils), which must subsequently be removed.
Using single-molecule techniques, we have studied both the physics of supercoil removal (Crut et al., PNAS 2007), as well as the activity of enzymes called topoisomerases, whose presence in the cell is required for effective supercoil removal. We have quantified the mechanism of type 1B topoisomerases and demonstrated that these enzymes employ a stochastic process that is torque-dependent (Koster et al., Nature 2005). Recently, we have generalized this mechanism to include additional enzymes such as DNA ligases (Crut et al., submitted).
We have also examined the effect of chemotherapeutic drugs on the rate of supercoil removal and observed a dramatic reduction in the rate of supercoil removal in the presence of topotecan, a drug in clinical use. We have consequently investigated whether supercoils accumulate in yeast cells and demonstrate such an accumulation in two phases of the cell cycle. These experiments provide a unique link between single-molecule studies on the one hand, and cellular processes on the other (Koster et al., Nature 2007). Time permitting, I will also discuss how these experiments on topoisomerases as well as others on RNA-dependent RNA polymerases (Vilfan et al., submitted) have lead to an increased interest in the laboratory in the mechanisms that cause molecular motors to stall.